1KXM

Crystal structure of Cytochrome c Peroxidase with a Proposed Electron Transfer Pathway Excised to Form a Ligand Binding Channel.

Structural Biology Knowledgebase: 1KXM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 1KXM

Classification: OXIDOREDUCTASE

Total Structure Weight: 33764.63

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome c Peroxidase A 290 Saccharomyces cerevisiae EC#: 1.11.1.5 IUBMB
Fragment: RESIDUES 72-362, NUMBERED 4-292
Mutation: P190G, ΔW259, ΔA261
Gene Name(s): CCP1 CCP CPO Gene View YKR066C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BZI
Query on BZI

A BENZIMIDAZOLE
C7 H6 N2
HYZJCKYKOHLVJF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BZI N/A in BindingDB
Kd: 140000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.194
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 106.50 α = 90.00
b = 75.00 β = 90.00
c = 50.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-02-01
  • Released Date: 2002-03-06
  • Deposition author(s): Rosenfeld, R.J., Hayes, A.M.A., Musah, R.A., Goodin, D.B.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4